Cation ordering in the 1322 perovskite CaCu3Fe2Nb2O12 has been investigated by synchrotron X-ray diffraction structure analysis, high-resolution electron microscopy, and magnetic measurements. All of the samples have full 1:3 ordering of Ca and Cu cations at the perovskite A-sites, but the Fe and Nb cations at the B sites show different degrees of ordering depending on the synthesis conditions. A slow-cooled sample has almost complete rock-salt-type 1:1 cation ordering at the B sites, but a rapidly cooled sample has no long-range B-cation arrangement. The ordered compound shows a large saturated magnetization (5.7 μB/formula unit (fu)) below 170 K due to the ferrimagnetism of the A′-site Cu2+ and B-site Fe3+ spins, whereas the B-site disordered form has a small magnetization (<1 μB/fu at 5 K). The degree of B-site cation order thus controls the magnetic behavior of 1322 CaCu3Fe2Nb2O12 perovskites.